Spectroscopic imaging has been implemented in a transmission electron microscope equipped with a post-column energy filter with the aim of obtaining quantitative elemental distributions and energy-loss spectra from biological specimens on a nanometer scale. Series of up to one hundred 1024x1024 pixel energy-selected images have been recorded with a cooled CCD camera coupled to a single crystal YAG scintillator situated at the image plane of the energy-filter. Individual images in each series are first cross-correlated to correct for specimen drift. Spectra are then extracted at each pixel and the net core-edge intensity is obtained by extrapolating the background and integrating the signal within a specified energy range. The advantage of spectrum-imaging over the conventional two-window or three-window EELS mapping techniques is the increased accuracy in estimating the background intensity. Furthermore, spectrum-imaging in the energy-filtering transmission electron microscope (EFTEM) can be used to acquire elemental maps from larger sample areas than is achievable in the scanning transmission electron microscope (STEM), although the minimum detectable concentrations are lower in the STEM. We have applied the spectrum-imaging technique in the EFTEM to map the distributions of sulfur-rich proteins in secretory cells.